I jumped ahead there and left a step of my reasoning out. The article describes a lack of backstock, due to OTS, causing out-of-stocks when stores have to miss a delivery or two. But if you assume that the vast majority of these issues were in fact caused by unpredictable events, then the only possible solution would be to keep large amounts of extra stock at all times, which is worse for the customer and the company in the end. Obviously the goal is for neither extreme to occur.
The article is wrong about the regularity of the issue, the "weird control systems" (not sure what connection you're seeing with employee protection laws), and the causes.
But you misunderstand me if you think I'm burying my head in the sand. I don't deny that Whole Foods has issues with its ordering processes. In fact, I think the company has been going in the wrong direction there for a long time. The article is just so, so off-base - originally I didn't intend to argue with it, but now I've become this guy: https://xkcd.com/386/
It will be interesting to see if Amazon can improve the situation through automation. Generally I've seen stores that use automated ordering systems be far worse with their out-of-stocks (Kroger, for instance).